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# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
inherit java-pkg-opt-2 java-ant-2 toolchain-funcs
MY_P=${PN}.${PV}
DESCRIPTION="Protein multiple-alignment-based sequence annealing"
HOMEPAGE="https://wiki.gentoo.org/wiki/No_homepage"
SRC_URI="http://baboon.math.berkeley.edu/${PN}/download/${MY_P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="java"
RDEPEND="java? ( >=virtual/jre-1.8:* )"
DEPEND="java? ( >=virtual/jdk-1.8:* )"
S=${WORKDIR}/${PN}-align
PATCHES=(
"${FILESDIR}"/${P}-makefile.patch
"${FILESDIR}"/${P}-includes.patch
)
src_prepare() {
default
java-pkg-opt-2_src_prepare
}
src_compile() {
emake -C align CXX="$(tc-getCXX)" OPT_CXXFLAGS="${CXXFLAGS}"
if use java; then
pushd display >/dev/null || die
eant -Ddisplay all || die
popd >/dev/null || die
fi
}
src_install() {
dobin align/${PN}
dodoc align/{README,PROBCONS.README}
insinto /usr/share/${PN}/examples
doins -r examples/.
if use java; then
java-pkg_newjar display/AmapDisplay.jar amapdisplay.jar
java-pkg_dolauncher amapdisplay --jar amapdisplay.jar
fi
}
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